Abstract
Metabolomics has developed into a major tool in functional genomics and plant systems biology. The various methods used for metabolomic analysis will be discussed from the analytical methods back to the preanalytical phase and the biological experiment. Particularly aspects of the preanalytical phase of the analysis is dealt with, including the risks of artefact formation with the various commonly used solvents. Metabolomics is like a snap shot, and conclusions from dynamic systems must be drawn with great care as demonstrated with a biosynthetic study of salicylate in Catharanthus roseus cell cultures.
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References
Baerheim Svendsen A, Karlsen J (1966) Direkte Gaschromatografie der Bestandteile der Aetherische Oelen in Pflanzenmaterial. Planta Medica 14:376
Baerheim Svendsen A, Verpoorte R (1983) Chromatography of alkaloids, part I, Thin-layer Chromatography, vol 23A. Chromatography Library, Elsevier, Amsterdam, 534 pp
Bisset NB, Choudhury AK (1974) Alkaloids and iridoids from Strychnos nux-vomica fruits. Phytochemistry 13:265–269
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FCP, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME) – toward standards for microarray data. Nat Genet 29:365–371
Breitling R, Ritchie S, Goodenowe D, Stewart ML, Barrett MP (2006) Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data. Metabolomics 2:155–164
Budi Muljono RA, Scheffer JJC, Verpoorte R (2002a) Isochorismate is an intermediate in 2,3-dihydroxybenzoic acid biosynthesis in Catharanthus roseus cell cultures. Plant Physiol Biochem 40:231–234
Budi Muljono RA, Talou JR, Scheffer JJC, Verpoorte R (2002b) Biosynthesis of 2,3-dihydroxybenzoic acid in transgenic Catharanthus roseus cell cultures overexpressing isochorismate synthase. Heterocycles 56:341–352
Choi YH, Kim HK, Linthorst HJM, Hollander JG, Lefeber AWM, Erkelens C, Nuzillard J-M, Verpoorte R (2006a) NMR metabolomics to revisit the tobacco mosaic virus infection in Nicotiana tabacum leaves. J Nat Prod 69:742–748
Choi YH, Kim HK, Verpoorte R (2006b) Metabolomics. In: Kayser O, Quax W (eds) Medicinal plant biotechnology from basic research to industrial applications. Wiley-VCH, Weinheim, pp 9–28
Cordell GA (1974) The biosynthesis of indole alkaloids. Lloydia 37:219–98
Dallüge J, Beens J, Brinkman UAT (2003) Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool. J Chromatogr A 1000:69–108
Day RC, Grossniklaus U, Macknight RC (2005) Be more specific! Laser-assisted microdissection of plant cells. Trends Plant Sci 10:397–406
Fiehn O (2003) Metabolic networks of Cucurbita maxima phloem. Phytochemistry 62:75–886
Gobey J, Cole M, Janiszewski J, Covey T, Chau T, Kovarik P, Corr J (2005) Characterization and performance of MALDI on a triple quadruple mass spectrometer for analysis and quantification of small molecules. Anal Chem 77:5463–5654
Hanson KR (1965) Chlorogenic acid biosynthesis. Chemical synthesis and properties of the mono-O-cinnamoylquinic acids. Biochemistry 4:2719–2731
Ioannidis JPA (2005) Why most published research findings are false. PLoS Med 2:696–701
Kim J, Choi YH, Yoo K-P (2001) Supercritical fluid extraction of alkaloids. In: Pelletier SW (ed) Alkaloids: chemical and biological perspectives. Pergamon Press, Amsterdam, pp 415–432
Kopka J (2006) Gas chromatography mass spectrometry. In: Saito K, Dixon RA, Willmitzer L (eds) Biotechnology in agriculture and forestry 57 plant metabolomics. Springer, Leipzig, pp 3–20
Lay JO Jr, Borgmann S, Liyanage R, Wilkins CL (2006) Problems with “Omics”. Trends Anal Chem 25:1046–1056
Liang Y-S, Lefeber AWM, Erkelens C, Kim HK, Choi YH, Verpoorte R (2006) Identification of phenylpropanoids in Brassica rapa leaves treated with methyl jasmonate using two-dimensional nuclear magnetic resonance spectroscopy. J Chromatogr A 1112:148–155
Lindon JC, Keun HC, Ebbels TMD, Pearce JMT, Holmes E, Nicholson JK (2005) The Consortium for Metabonomic Toxicology (COMET): aims, activities and achievements. Pharmacogenomics 6:691–699
Looser R, Krotzky A, Trethewey RN (2005) Metabolite profiling with GC-MS and LC-MS. In: Vaidyanathan S, Harrigan G, Goodacre R (eds) Metabolome analyses strategies for systems biology. Springer, New York, pp 103–118
Marsh KN, Boxall JA, Lichtenthaler R (2004) Room temperature ionic liquids and their mixtures – a review. Fluid Phase Equilib 219:93–98
Maudens KE, Wille SMR, Lambert WE (2007) Traces of phosgene in chloroform: consequences for extraction of anthracyclines. J Chromatogr B 848:384–390
Moco S, Bino RJ, Vorst O, Verhoeven HA, De Groot J, Van Beek TA, Vervoort J, De Vos CHR (2006) A liquid chromatography-mass spectrometry-based metabolome database for tomato. Plant Physiol 141:1205–1218
Moreno PRH, Van der Heijden R, Verpoorte R (1994) Elicitor-mediated induction of isochorismate synthase and accumulation of 2,3-dihydroxybenzoic acid in Catharanthus roseus cell suspension and shoot cultures. Plant Cell Rep 14:188–191
Mustafa NR (2007) Retrobiosynthetic study of salicylic acid in Catharanthus roseus cell suspension cultures. PhD thesis, Leiden University, Leiden
Pauli GF, Jaki BU, Lankin DC (2005) Quantitative 1H NMR: development and potential of a method for natural products analysis. J Nat Prod 68:133–149
Reily MD, Lindon JC (2005) NMR spectroscopy: principles and instrumentation. In: Robertson DG, Lindon J, Nicholson JK, Holmes E (eds) Metabonomics in toxicity assessment. CRC Press, Boca Raton, pp 75–104
Ryan D, Robards K (2006) Metabolomics: the greatest omics of them all? Anal Chem 78:7954–7958
Santos FJ, Galceran MT (2003) Modern developments in gas chromatography-mass spectrometry-based environmental analysis. J Chromatogr A 1000:125–151
Schripsema J, Verpoorte R (1991) Investigation of extracts of plant cell cultures by 1H NMR. Phytochem Anal 2:155–162
Schripsema J, Erkelens C, Verpoorte R (1991) Intra- and extracellular carbohydrates in plant cell cultures investigated by 1H-NMR. Plant Cell Rep 9:527–530
Seddon KR (1997) Ionic liquids for clean technology. J Chem Tech Biotechnol 68:351–356
Snyder LR (1974) Role of the solvent in liquid-solid chromatography – a review. Anal Chem 46:1384–1393
Sumner LW, Mendes P, Dixon R (2003) Plant metabolomics: large-scale phytochemistry in the functional genomics era. Phytochemisty 62:817–836
Taylor J, King RD, Altmann T, Fiehn O (2002) Application to metabolomics to plant genotype discrimination using statistics and machine learning. Plant J 18:241–248
Van Tegelen LJP, Bongaerts RJM, Croes AF, Verpoorte R, Wullems GJ (1999a) Isochorismate synthase isoforms from elicited cell suspension cultures of Rubia tinctorum. Phytochemistry 51:263–269
Van Tegelen LJP, Moreno PRH, Croes AF, Verpoorte R, Wullems GJ (1999b) Purification and cDNA cloning of Isochorismate synthase from elicited cell suspension cultures of Catharanthus roseus. Plant Physiol 119:705–712
Verberne MC, Budi Muljono RA, Verpoorte R (1999) Salicylic acid biosynthesis. In: Hooykaas PJJ, Hall MA, Libbenga KR (eds) Biochemistry and molecular biology of plant hormones. New comprehensive biochemistry, vol 33. Elsevier, Amsterdam, pp 295–312
Verberne M, Verpoorte R, Bol J, Mercado-Blanco J, Linthorst HJM (2000) Overproduction of salicylic acid in plants by bacterial transgenes enhances pathogen resistance. Nat Biotechnol 18:779–783
Verberne MC, Brouwer N, Delbianco F, Linthorst HJM, Bol JF, Verpoorte R (2002) Method for the extraction of the volatile compound salicylic acid from tobacco leaf material. Phytochem Anal 13:45–50
Verpoorte R, Baerheim Svendsen A (1976) The alkaloids of Strychnos dolichothyrsa. J Nat Prod 39:357–362
Verpoorte R, Baerheim Svendsen A (1978) Alkaloids from Strychnos dolichothyrsa. J Pharm Sci 67:171–174
Verpoorte R, Baerheim Svendsen A (1984) Chromatography of alkaloids, part II. Gas and liquid chromatography, vol 23B. Chromatography Library, Elsevier, Amsterdam, 534 pp
Verpoorte R, Choi YH, Kim HK (2007) NMR-based metabolomics at work in phytochemistry. Phytochem Rev 6:3–14
Wagner C, Sefkow M, Kopka J (2003) Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemisty 62:887–900
Xianlin Han, Gross RW (2003) Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. J Lipid Res 44:1071–1079
Yamazaki Y, Kitajima M, Arita M, Takayama H, Sudo H, Yamazaki M, Aimi N, Saito K (2004) Biosynthesis of Camptothecin in silico and in vivo tracer study from [1-13C] Glucose. Plant Physiol 134:161–170
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Verpoorte, R., Choi, Y.H., Mustafa, N.R. et al. Metabolomics: back to basics. Phytochem Rev 7, 525–537 (2008). https://doi.org/10.1007/s11101-008-9091-7
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DOI: https://doi.org/10.1007/s11101-008-9091-7